It depends on what do you mean by "disable".
If you mean you want physically DELETE those ships from the game so no faction fleet ever use them, I think you can edit the faction files to change their fleet composition, which requires some knowledge about game file but not really a worthy issue to create a mod for it.
If you, like what I'm thinking, mean you want some new ship that particularly countering phased ships by disabling them while they are phased (kinda like the quantum disruptor ship system), I've done my research and it seems there's no such ship in the 0.9 mods I have played.
I've done the research because i am annoyed by phase ships just like you. Phase ships are fast and you can't chase them down, they are immune to damage except the 1 second time window when they launch their alpha-strike to destroy your ships, and they choose when to engage the combat, not you. The fact that you can't stop them from running away to safely vent flux is kind of frustrating.
Therefore I've decided to make a ship with a ship system that disable nearby phased ship by force them to overload. And I just shared my ideas with friends on discord. However, it turns out I'm not seeing the whole picture...
To conclude the discussion I had on discord, in general, phased ship are not significantly stronger than other ships. they have their unique advantage, but also have some disadvantage in their design to compensate for that, like fewer weapon slots, less hull/armor, bad logistic stats. Plus they can be countered by carriers and good tracking missiles. There is no need to particularly counter phased ship, especially by disabling they phased status, which is considered almost an insta-kill.
In addition, I believe there are a lot players like playing as a phased ship, I don't think any existing mod want to punish phase ships too much. From my game experience, enemy phased ship only give me trouble in very early game. once i got my first few carriers, I can handle them properly (I mean only the vanilla phase ships, not sure how powerful phased ship are in mods).
I would suggest you just try to learn how to deal with phase ships as you play the game, taking them out of the game will also take out a lot of fun fighting as or against them.
Of course, you can always edit the faction files to delete phased ship, if you choose to do so.